Animate .stl files in Blender
I do not have a straight out easy solution, but i can think of a 2 ways of doing this. 

Do all the STL files have the same number of Vertices and faces? 

If the number of Vertices and Faces dont change, I would suggest a python script.

first have a look at the AnimAll addon that comes with blender. you just have to enable it in your user preferences.

http://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Animation/AnimAll

write a script that does the following:


imports the first STL frame.
call:


  bpy.ops.anim.insert_keyframe_animall()

then for each frame after that:


import the STL File for that frame.
change the positions of each vertex in the main object to that in the frame imported.
call:


  bpy.ops.anim.insert_keyframe_animall()
  delete the STL frame imported.
  



That way all your frames will be in the same object, and show up as keyframes in the animation editors.

This assumes that the STL files have kept the vertices order the same, otherwise this method will not work and your imported animation will just jump all over the place.

There is the MeshFoot addon which will import a sequence of OBJ files, however it does not work with STL files, so you would have to modify the code to get it working with STL files.